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TABLE 1. Codons known to undergo HM mutations during propagation in egg culture

Codon

Rbs

AB

PosSel

111

0

0

0

126

0

1

0

137

1

1

0

138

1

1

1

144

0

1

0

145

0

1

1

155

1

1

0

156

0

1

1

158

0

1

1

159

0

1

0

185

0

0

0

186

0

1

1

193

0

1

1

194

1

1

1

199

0

0

0

219

0

0

0

226

1

0

1

229

0

0

0

246

0

0

0

248

0

0

0

276

0

0

0

290

0

0

0

Five of the 22 HM codons known to undergo HM mutations during propagationin egg culture are associated with the HA sialic acid receptor bindingsite (Rbs), 12 HM codons are in or near antibody combining sitesA or B (AB). Eight HM codons have been identified as having beenunder positive selection (PosSel) to change the amino acid they encodedin the past (Bush et al., 1999).

If mutations were assigned to terminal and internal branches in proportion to the relative number of each branch type, we would expect to have 12 mutations assigned to the terminal branches. However, we observed 15 mutations on the terminal branches, an excess of 25% over expectations. Thus intentionally sampling with a bias toward genetically divergent isolates results in those isolates being attached to the tree by longer branches than if their close relatives were also in the sample.

Unlike the excess mutations assigned to terminal branches that are caused by HM change, the excess caused by sampling bias is not of concern with respect to the evolutionary inference one might draw from the tree. Apportioning excess terminal branch lengths to the two different hypotheses is easily illustrated in a cartoon such as Fig. 2. In reality, we know that we have observed an excess of mutations on the terminal branches; however, we don't know precisely which branches or mutations are involved. In this paper we show how to determine the proportion, but not the actual



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